Detailed information of evm.model.HiC_scaffold_24.53 in Chrysaora quinquecirrha

Genomic Location: HiC_scaffold_24:350112...352208
NR annotation: CAG9565363.1, unnamed protein product [Danaus chrysippus]
Species Chrysaora quinquecirrha · all data for this species · gene families


 Gene Structure
More details in JBrowse  Sequence
CDS
Transcript
Protein
 UniProt (Swiss-Prot top hit)
UniProt accessionDescription
P35072Transposable element Tcb1 transposase OS=Caenorhabditis briggsae OX=6238 PE=3 SV=1
P34257Transposable element Tc3 transposase OS=Caenorhabditis elegans OX=6239 GN=tc3a PE=1 SV=1
 Gene family
Family typeMembership / link
Orthogroup (gene family)OG0000182 (this species only) · gene tree & orthology
Ubiquitin familyE3|E3 activity|HECT · all ubiquitin genes in this species

 Pfam domain
Pfam accessionPfam nameDescriptionTypeSource
PF13936
all species →
HTH_38Helix-turn-helix domainDomainInterproscan
PF13358
all species →
DDE_3DDE superfamily endonucleaseDomainInterproscan
PF01498
all species →
HTH_Tnp_Tc3_2TransposaseFamilyInterproscan

 InterPro
InterPro termTypeDescriptionSource
IPR036397
all species →
Homologous_superfamilyRibonuclease H superfamilyInterproscan
IPR025246
all species →
DomainTransposase IS30-like HTH domainInterproscan
IPR009057
all species →
Homologous_superfamilyHomeobox-like domain superfamilyInterproscan
IPR035983
all species →
Homologous_superfamilyHECT, E3 ligase catalytic domainInterproscan
IPR038717
all species →
DomainTc1-like transposase, DDE domainInterproscan
IPR036388
all species →
Homologous_superfamilyWinged helix-like DNA-binding domain superfamilyInterproscan
IPR000569
all species →
DomainHECT domainInterproscan
IPR002492
all species →
DomainTransposase, Tc1-likeInterproscan
IPR052338
all species →
FamilyTransposase_5Interproscan

 PANTHER
PANTHER termDescriptionSource
PTHR23022
all species →
TRANSPOSABLE ELEMENT-RELATEDInterproscan

 Gene Ontology
GO termCategoryDescriptionSource
GO:0003676
all species →
Molecular Functionnucleic acid bindingInterproscan
GO:0004842
all species →
Molecular Functionubiquitin-protein transferase activityInterproscan
GO:0003677
all species →
Molecular FunctionDNA bindingInterproscan
GO:0006313
all species →
Biological ProcessDNA transpositionInterproscan
GO:0015074
all species →
Biological ProcessDNA integrationInterproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.
 KEGG pathway
No KEGG orthology assignment for evm.model.HiC_scaffold_24.53.

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Co-expression network

Genes whose expression across the transcriptome samples of Chrysaora quinquecirrha tracks this one. Counts are over the whole network; the network view itself draws at most 100 partners per query gene (CNIDO_NET_TOP_K), so a hub gene can show fewer edges than the number below.

No co-expression network has been built for this species, so this gene has no partners to show. Networks are available for the species listed on the Network Analysis page.

Single-cell expression

Whether this gene can be visualised in the single-cell atlases of Chrysaora quinquecirrha, and in which cell types it is a marker. Expression is stored per cell, so the violin plot and the cell-type means are computed in the viewer — open a dataset to see them.

No single-cell dataset has been published for this species. The atlases that do exist are listed in the Cell Atlas.

Epigenetic marks

Chromatin and DNA-methylation data covering this gene. Peak calls are listed per sample with the genomic region the peak falls in; DNA methylation is listed as sample availability only, because those tables are queried by the DNA Methylation page itself.

No epigenomic data has been deposited for this species. The assays that exist across the site are described in the Epigenomic Data module.

What you can do with this gene

Every tool below opens with this gene already entered, so you land on the analysis rather than on an empty form. Links open in a new tab.

AnalysisWhat it doesStatus
Primer designDesign PCR / qPCR primers on this gene’s sequence with the published primer3 settings. Opens with the primers already computed.template foundopen →
BLASTSearch this gene’s sequence against the CnidoSite BLAST databases. The query is filled in and the species’ database is preselected — press Run to start.template foundopen →
Expression heatmapDraw this gene’s expression as a heatmap across all RNA-seq samples, and compare it with the genes you add next to it.no expression matrix
Gene family / orthogroupLook this gene up in the single-copy orthogroups built from the high-quality cnidarian genomes, and see which other species carry an orthologue.open →
Gene set analysisStart a gene-set enrichment analysis with this gene as the seed list. Add more genes on that page before running it.open →
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